BN1752 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 8.2112e-05 1.2849e-03
Layer 4 9.8480e-05 1.2595e-03
Layer 1 1.6800e-03 8.8245e-02
Layer 6 1.8349e-03 7.5610e-03
Layer 3 1.9046e-03 9.4624e-02
Layer 2 2.5196e-03 1.0344e-01
WM 9.6959e-01 5.6010e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
STMN2 Expression Distribution
Gene Specificity Score (GSS)
STMN2 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
STMN2 Layer 5 2.9805 0.6384
SNCA Layer 5 2.5059 0.6266
SYN2 Layer 5 2.5635 0.6206
TUBB2A Layer 5 2.5664 0.6204
NEFL Layer 5 2.7012 0.6139
EEF1A2 Layer 5 2.5449 0.6078
TPPP Layer 5 2.1543 0.6033
STMN1 Layer 4 2.5781 0.6015
PRKAR1B Layer 4 2.5449 0.5973
ATP1B1 Layer 5 2.3027 0.5958
NAPB Layer 4 2.4395 0.5885
NSF Layer 5 2.4297 0.5876
PPP2R1A Layer 4 2.3027 0.5867
HK1 Layer 5 2.1055 0.5863
NDRG4 Layer 5 2.5449 0.5860
TAGLN3 Layer 5 2.3594 0.5854
RTN1 Layer 5 2.4395 0.5849
VAMP2 Layer 5 2.3867 0.5815
YWHAG Layer 5 2.3652 0.5811
MLLT11 Layer 5 2.2832 0.5805
CHGA Layer 4 2.7910 0.5776
RAB6B Layer 5 2.3711 0.5767
APBB1 Layer 4 2.2266 0.5763
TOLLIP Layer 5 2.3184 0.5742
NDFIP1 Layer 5 2.1543 0.5732
GDI1 Layer 4 2.2002 0.5732
NUCKS1 Layer 5 2.2363 0.5730
AGAP3 Layer 5 2.3086 0.5729
RNF11 Layer 5 2.3555 0.5725
SNCG Layer 5 2.6016 0.5706
GPI Layer 5 2.2930 0.5704
DNM1 Layer 4 2.5029 0.5701
SOD2 Layer 5 2.3750 0.5698
YWHAE Layer 4 2.2363 0.5694
KLC1 Layer 5 2.2871 0.5692
CELF4 Layer 5 2.4082 0.5688
MAP1A Layer 5 2.2832 0.5686
TUBB4B Layer 4 2.7246 0.5678
SYT4 Layer 5 2.4268 0.5665
RTN3 Layer 5 2.3242 0.5641
CALM3 Layer 4 2.2832 0.5636
HPCA Layer 4 2.7480 0.5636
SPOCK2 Layer 5 2.2324 0.5630
SYT1 Layer 4 2.3086 0.5625
SH3GL2 Layer 4 2.2930 0.5609
MTCH1 Layer 5 2.2773 0.5608
NORAD Layer 4 2.3184 0.5607
SOD1 Layer 5 2.1748 0.5607
PNMA2 Layer 5 2.3086 0.5605
SSBP3 Layer 4 2.3057 0.5598

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1752
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1752_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1752/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1752/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1752/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1752/report/PD/BN1752_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1752/report/PD/BN1752_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 06:58:02
  • Number of Processes: 10
  • Spending Time: 0h 3m